Is GRPR p.Val384= (c.1152C>G) pathogenic?

GRPR p.Val384= (c.1152C>G) is classified Likely benign in GRPR (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-06). Rare (popmax 0.15%, afr).

How common is GRPR p.Val384= (c.1152C>G) in the general population?

GRPR p.Val384= (c.1152C>G) is rare (popmax 0.15%, afr) (gnomAD).

GRPR p.Val384=

c.1152C>G · rs112179848 · VCV745044

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.15%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.31	GERP -2.3, phastCons 0.99
Overall
CADD	3.348	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.15% African / African-American · 85/56,743 alleles

Filtering AF 0.124% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.115%

Overall 0.0124% 149/1,204,851 alleles · rare exomes 110/1,094,174 · genomes 39/110,677 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.15%	668
Remaining individualsnot grpmax-eligible	0.12%	833
Middle Eastern	0.0461%	2,169
Admixed American	0.00219%	45,593
South Asian	0.00177%	56,609
European (non-Finnish)	0.000337%	297,135

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GRPR
Protein: p.Val384=
Coding: c.1152C>G
MANE Select: NM_005314
dbSNP: rs112179848
Type: single nucleotide variant
Location: chrX:16152642 (GRCh38)
Structure: AlphaFold pLDDT 78.78 · 4 PDB

Full GRPR gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GRPR p.Lys362= Likely benign ★★ same type
GRPR p.Thr132= Benign ★★ same type
GRPR p.Val220Ile Likely benign ★★ same type
GRPR p.Ala136Val Uncertain significance ★ ⚠ same type
GRPR p.Ala369Val Uncertain significance ★ ⚠ same type
GRPR p.Arg144Trp Uncertain significance ★ ⚠ same type
GRPR p.Arg261Gln Uncertain significance ★ ⚠ same type
GRPR p.Arg287Leu Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/grpr-p-val384 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown